# Bio.SeqIO.FastaIO module

Bio.SeqIO support for the “fasta” (aka FastA or Pearson) file format.

You are expected to use this module via the Bio.SeqIO functions.

Bio.SeqIO.FastaIO.SimpleFastaParser(handle)

  Iterate over Fasta records as string tuples.

  Arguments:

    - handle - input stream opened in text mode

  For each record a tuple of two strings is returned, the FASTA title line (without the leading ‘>’ character), and the sequence (with any whitespace removed). The title line is not divided up into an identifier (the first word) and comment or description.

      >>> with open("Fasta/dups.fasta") as handle:
      ...     for values in SimpleFastaParser(handle):
      ...         print(values)
      ...
      ('alpha', 'ACGTA')
      ('beta', 'CGTC')
      ('gamma', 'CCGCC')
      ('alpha (again - this is a duplicate entry to test the indexing code)', 'ACGTA')
      ('delta', 'CGCGC')

Bio.SeqIO.FastaIO.FastaTwoLineParser(handle)

  Iterate over no-wrapping Fasta records as string tuples.

  Arguments:

    - handle - input stream opened in text mode

  Functionally the same as SimpleFastaParser but with a strict interpretation of the FASTA format as exactly two lines per record, the greater-than-sign identifier with description, and the sequence with no line wrapping.

  Any line wrapping will raise an exception, as will excess blank lines (other than the special case of a zero-length sequence as the second line of a record).

  Examples

  This file uses two lines per FASTA record:

      >>> with open("Fasta/aster_no_wrap.pro") as handle:
      ...     for title, seq in FastaTwoLineParser(handle):
      ...         print("%s = %s..." % (title, seq[:3]))
      ...
      gi|3298468|dbj|BAA31520.1| SAMIPF = GGH...

  This equivalent file uses line wrapping:

      >>> with open("Fasta/aster.pro") as handle:
      ...     for title, seq in FastaTwoLineParser(handle):
      ...         print("%s = %s..." % (title, seq[:3]))
      ...
      Traceback (most recent call last):
         ...
      ValueError: Expected FASTA record starting with '>' character. Perhaps this file is using FASTA line wrapping? Got: 'MTFGLVYTVYATAIDPKKGSLGTIAPIAIGFIVGANI'

class Bio.SeqIO.FastaIO.FastaIterator(source: IO[str] | PathLike | str | bytes, alphabet: None = None)

  Bases: `SequenceIterator`

  Parser for plain Fasta files without comments.

  modes = 't'
  __init__(source: IO[str] | PathLike | str | bytes, alphabet: None = None) → None

    Iterate over Fasta records as SeqRecord objects.

    Arguments:

      - source - input stream opened in text mode, or a path to a file

      - alphabet - optional alphabet, not used. Leave as None.

    This parser expects a plain Fasta format without comments or header lines.

    By default this will act like calling Bio.SeqIO.parse(handle, “fasta”) with no custom handling of the title lines:

        >>> with open("Fasta/dups.fasta") as handle:
        ...     for record in FastaIterator(handle):
        ...         print(record.id)
        ...
        alpha
        beta
        gamma
        alpha
        delta

    If you want to modify the records before writing, for example to change the ID of each record, you can use a generator function as follows:

        >>> def modify_records(records):
        ...     for record in records:
        ...         record.id = record.id.upper()
        ...         yield record
        ...
        >>> with open('Fasta/dups.fasta') as handle:
        ...     for record in modify_records(FastaIterator(handle)):
        ...         print(record.id)
        ...
        ALPHA
        BETA
        GAMMA
        ALPHA
        DELTA

  __next__()

    Return the next SeqRecord.

    This method must be implemented by the subclass.

  __abstractmethods__ = frozenset({})
  __annotations__ = {}
  __firstlineno__ = 143
  __parameters__ = ()
  __static_attributes__ = ('_line',)

class Bio.SeqIO.FastaIO.FastaTwoLineIterator(source)

  Bases: `SequenceIterator`

  Parser for Fasta files with exactly two lines per record.

  modes = 't'
  __init__(source)

    Iterate over two-line Fasta records (as SeqRecord objects).

    Arguments:

      - source - input stream opened in text mode, or a path to a file

    This uses a strict interpretation of the FASTA as requiring exactly two lines per record (no line wrapping).

    Only the default title to ID/name/description parsing offered by the relaxed FASTA parser is offered.

  __next__()

    Return the next SeqRecord.

    This method must be implemented by the subclass.

  __abstractmethods__ = frozenset({})
  __annotations__ = {}
  __firstlineno__ = 268
  __parameters__ = ()
  __static_attributes__ = ('_data',)

class Bio.SeqIO.FastaIO.FastaBlastIterator(source: IO[str] | PathLike | str | bytes, alphabet: None = None)

  Bases: `SequenceIterator`

  Parser for Fasta files, allowing for comments as in BLAST.

  modes = 't'
  __init__(source: IO[str] | PathLike | str | bytes, alphabet: None = None) → None

    Iterate over Fasta records as SeqRecord objects.

    Arguments:

      - source - input stream opened in text mode, or a path to a file

      - alphabet - optional alphabet, not used. Leave as None.

    This parser expects the data to be in FASTA format. As in BLAST, lines starting with ‘#’, ‘!’, or ‘;’ are interpreted as comments and ignored.

    This iterator acts like calling Bio.SeqIO.parse(handle, “fasta-blast”) with no custom handling of the title lines:

        >>> with open("Fasta/dups.fasta") as handle:
        ...     for record in FastaIterator(handle):
        ...         print(record.id)
        ...
        alpha
        beta
        gamma
        alpha
        delta

    If you want to modify the records before writing, for example to change the ID of each record, you can use a generator function as follows:

        >>> def modify_records(records):
        ...     for record in records:
        ...         record.id = record.id.upper()
        ...         yield record
        ...
        >>> with open('Fasta/dups.fasta') as handle:
        ...     for record in modify_records(FastaIterator(handle)):
        ...         print(record.id)
        ...
        ALPHA
        BETA
        GAMMA
        ALPHA
        DELTA

  __next__()

    Return the next SeqRecord.

    This method must be implemented by the subclass.

  __abstractmethods__ = frozenset({})
  __annotations__ = {}
  __firstlineno__ = 304
  __parameters__ = ()
  __static_attributes__ = ('_line',)

class Bio.SeqIO.FastaIO.FastaPearsonIterator(source: IO[str] | PathLike | str | bytes, alphabet: None = None)

  Bases: `SequenceIterator`

  Parser for Fasta files, allowing for comments as in the FASTA aligner.

  modes = 't'
  __init__(source: IO[str] | PathLike | str | bytes, alphabet: None = None) → None

    Iterate over Fasta records as SeqRecord objects.

    Arguments:

      - source - input stream opened in text mode, or a path to a file

      - alphabet - optional alphabet, not used. Leave as None.

    This parser expects a Fasta format allowing for a header (before the first sequence record) and comments (lines starting with ‘;’) as in William Pearson’s FASTA aligner software.

    This iterator acts as calling Bio.SeqIO.parse(handle, “fasta-pearson”) with no custom handling of the title lines:

        >>> with open("Fasta/dups.fasta") as handle:
        ...     for record in FastaIterator(handle):
        ...         print(record.id)
        ...
        alpha
        beta
        gamma
        alpha
        delta

    If you want to modify the records before writing, for example to change the ID of each record, you can use a generator function as follows:

        >>> def modify_records(records):
        ...     for record in records:
        ...         record.id = record.id.upper()
        ...         yield record
        ...
        >>> with open('Fasta/dups.fasta') as handle:
        ...     for record in modify_records(FastaIterator(handle)):
        ...         print(record.id)
        ...
        ALPHA
        BETA
        GAMMA
        ALPHA
        DELTA

  __next__()

    Return the next SeqRecord.

    This method must be implemented by the subclass.

  __abstractmethods__ = frozenset({})
  __annotations__ = {}
  __firstlineno__ = 403
  __parameters__ = ()
  __static_attributes__ = ('_line',)

class Bio.SeqIO.FastaIO.FastaWriter(target, wrap=60, record2title=None)

  Bases: `SequenceWriter`

  Class to write Fasta format files (OBSOLETE).

  Please use the `as_fasta` function instead, or the top level `Bio.SeqIO.write()` function instead using `format="fasta"`.

  modes = 't'
  __init__(target, wrap=60, record2title=None)

    Create a Fasta writer (OBSOLETE).

    Arguments:

      - target - Output stream opened in text mode, or a path to a file.

      - wrap - Optional line length used to wrap sequence lines. Defaults to wrapping the sequence at 60 characters Use zero (or None) for no wrapping, giving a single long line for the sequence.

      - record2title - Optional function to return the text to be used for the title line of each record. By default a combination of the record.id and record.description is used. If the record.description starts with the record.id, then just the record.description is used.

    You can either use:

        handle = open(filename, "w")
        writer = FastaWriter(handle)
        writer.write_file(myRecords)
        handle.close()

    Or, follow the sequential file writer system, for example:

        handle = open(filename, "w")
        writer = FastaWriter(handle)
        ...
        Multiple writer.write_record() and/or writer.write_records() calls
        ...
        handle.close()

  write_record(record)

    Write a single Fasta record to the file.

  __abstractmethods__ = frozenset({})
  __annotations__ = {}
  __firstlineno__ = 495
  __parameters__ = ()
  __static_attributes__ = ('record2title', 'wrap')

class Bio.SeqIO.FastaIO.FastaTwoLineWriter(handle, record2title=None)

  Bases: `FastaWriter`

  Class to write 2-line per record Fasta format files (OBSOLETE).

  This means we write the sequence information without line wrapping, and will always write a blank line for an empty sequence.

  Please use the `as_fasta_2line` function instead, or the top level `Bio.SeqIO.write()` function instead using `format="fasta"`.

  __init__(handle, record2title=None)

    Create a 2-line per record Fasta writer (OBSOLETE).

    Arguments:

      - handle - Handle to an output file, e.g. as returned by open(filename, “w”)

      - record2title - Optional function to return the text to be used for the title line of each record. By default a combination of the record.id and record.description is used. If the record.description starts with the record.id, then just the record.description is used.

    You can either use:

        handle = open(filename, "w")
        writer = FastaWriter(handle)
        writer.write_file(myRecords)
        handle.close()

    Or, follow the sequential file writer system, for example:

        handle = open(filename, "w")
        writer = FastaWriter(handle)
        ...
        Multiple writer.write_record() and/or writer.write_records() calls
        ...
        handle.close()

  __abstractmethods__ = frozenset({})
  __annotations__ = {}
  __firstlineno__ = 574
  __parameters__ = ()
  __static_attributes__ = ()

Bio.SeqIO.FastaIO.as_fasta(record)

  Turn a SeqRecord into a FASTA formatted string.

  This is used internally by the SeqRecord’s .format(“fasta”) method and by the SeqIO.write(…, …, “fasta”) function.

Bio.SeqIO.FastaIO.as_fasta_2line(record)

  Turn a SeqRecord into a two-line FASTA formatted string.

  This is used internally by the SeqRecord’s .format(“fasta-2line”) method and by the SeqIO.write(…, …, “fasta-2line”) function.

Biopython v: 1.85

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